POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets.

ABSTRACT: Functionally associated genes tend to be co-expressed, which indicates that they could also be co-regulated. Since co-regulation is usually governed by transcription factors via their specific binding elements, putative regulators can be identified from promoter sets of (co-expressed) genes by screening for over-represented nucleotide patterns. Here, we present a program, POCO, which discovers such over-represented patterns from either one or two promoter sets. Typical microarray experiments yield up- and down-regulated gene sets that may represent, for example, distinct defense pathways. Assuming that a functional transcription factor cannot simultaneously both up- and down-regulate the gene sets, its binding element should respectively be over- and under-represented in the corresponding

SUBMITTER: Kankainen M 

PROVIDER: S-EPMC1160228 | biostudies-literature | 2005 Jul

REPOSITORIES: biostudies-literature